Missing In Action
by eala-captian
Summary: Special Agent Emma Swan had the life any FBI agent wanted, and a partner who would lay his life on the line for her. Until one day two years ago it all came crashing down. Trying to pick up the pieces of her life and learning that things aren't always what they seem, Emma sets out to find the truth among the lies. Only sometimes the truth is easier left buried in the past.
1. Prologue

**Notes: This is honestly the first thing I've ever written. Ever. It's very short, and mostly just the thoughts I've had upstairs needing to be put on paper. I've been working on an archive project, and the detective trope interested me. This is an idea I've had stewing in my head for a few weeks now. I have no idea where this is going to go. If anywhere, but I'm gonna give it a shot. Keep on the lookout. I'm eala-captian on tumblr. All mistakes are my own..**

 **Disclaimer: I do not own any of the characters in this fic, but playing with them has become a new favorite pastime.**

Special Agent Emma Swan spent her 34th birthday the same way she had for the past three years, pouring over case files in her home. Their home. The home they built together in the small suburb around DC. Sitting her second tumbler full of rum on the counter she picked up one last case file. A file that had been haunting her every thought for almost two years. The picture at the top of the file didn't do him justice. His hair was shorter than normal and the scruff she had come to love was trimmed and neat. He looked younger in the photo, more carefree than the last time she saw his face. Even that was over the small computer screen in the conference room. Not much closure there.

 _Killian Jones, Former Special Agent MI6, Served four tours in hot zones with The Royal_

 _Navy, Partnership with FBI from United Nations, Highly trained in special ops,_

 _Specializing in interrogation and undercover operations._

 _May 17, 2013_

 _Agent Killian Jones has been successfully planted among the group know as The Dark Ones under alias Hook. This group is know to be linked to a string of kidnappings and human trafficking. Agent Jones reported at 17:00. Next report is scheduled with his handler and partner Emma Swan, Wednesday April,1 2013 at 19:00._

The list of reports went on and on. Until the last one. March 22, 2014. Then contact with Killian stopped. Almost as if he disappeared off the face of the planet.

Slamming the file back down onto the table, Emma picked up her glass and drank. It was what the file didn't say that hurt her the most. Killian Jones, Husband, Brother, Friend, Partner, loved, missed….The big red letters stamped over the cover tore her apart every time she dare close the file.

 _Missing…..._


	2. Chapter 1

**Notes: Whew its been an awesome week writing and researching for this chapter. Fair warning this chapter and the next few are going to be pretty intense. Establishing the seriousness of what Killian has gotten himself into was very draining and hurt me to write but it had to be done. Nothing More was playing on repeat the whole time I wrote this chapter. Check them out!**

 **Warning: This chapter contains torture and drug abuse.**

 **Disclaimer: Nope**

 _Monday October 27, 2008 Federal Bureau Of Investigation DC office 08:00_

Today had been a terrible day and it was only 08:00. Emma had, of course, woke up late after a long Sunday night out with Ruby. Ruby had a knack for getting her into all sorts of trouble. Today however, was not the day to be tardy or hungover. Today she was meeting her new partner. A MI6 agent on loan via the UN. They had been assigned a special task of looking into a small cell of smugglers with a knack for getting young women out of Europe and the Americas to Mexico City. From there they were spread all over the world, being used as everything from slaves to prostitutes. Her new partner Killian Jones has been following the group for several months now.

"I owe you a hangover for last night" Emma said as she slid into her desk beside Ruby. "Why is it that you always seem to want to party on the most inconvenient nights of the year?" Ruby smirked and shrugged her shoulders,"Maybe because today is a big day. I've been hearing lots of stuff down the grapevine about your new partner" she said "Apparently he is quite the looker and his record is very impressive." A commotion from across the room made them all look up with quiet anticipation. David Nolan who was the head of the office was standing near the front on the bullpen with the newcomer.

"Can I have everyone's attention, I'd like to introduce everyone to our new acting field agent, Killian Jones" From behind David a man stepped into view. Emma spared a glance at Ruby whose mouth had dropped open in astonishment. She reached over her desk and firmly pressed Ruby's mouth closed whispering "Really Red?" Under her breath. "Do you see this man?" Ruby questioned back.

Yes, yes Emma saw him. Piercing blue eyes looking right at her, how could she miss him. His hair was in a disarray almost as if he had just rolled out of bed and walked right on into work. She'd like to see him in the morning to compare. Whoa….Where did that come from? He wore a black button up shirt with the first few buttons undone. She could see small amounts of chest hair peaking out. He had his sleeves rolled up to his elbows. His left hand buried in his front pocket and his right through a belt loop right at the front. Ruby's information had been spot on. He _was_ quite the looker. Then he spoke "Thanks for the introduction David, I'm glad to be here and I'm hoping to get to work with all of you at some point in time. I know the reason I'm here isn't under the best circumstances, but there is a job to be done. And MI6 and the FBI have seen fit to join forces on this particular task. I hope to be meeting you all. Cheers." And with a small nod to David he stepped back into the shadows. "Emma can you meet me in my office?" Dave gave her a small smile before heading to the back of the bullpen. Killian followed with a smirk on his face.

"Well, you going to go or just sit there with that shit eating grin on your face?" Ruby said with a laugh. Oh she was going no doubt, but damn that smirk. That smirk made her feel things she hadn't thought about in years. It excited and scared her at the same time. With one final glance at Ruby, Emma stood and walked slowly towards the future.

 _Friday July, 29 2016 Oran, Algeria 07:00_

He was so comfortable. He could feel the sun seeping through the curtains in the house making a golden glow across the white bedspread. A comfortable warmth pressed tight against his left side. Rolling over he pried open his eyes to be met with a smiling face and a mass of blonde hair. He wrapped his right arm around her and pulled her tight into his chest. His Emma. His partner. His wife. His happiness.

"Hook, Hook" A voice broke into his peaceful comfort. "Wake the hell up." And just like that the dream was broken as he came rushing back to the harsh light of reality. Well Fuck. Emma had once again been ripped from his grasp. Being unconscious was the only place he could find her anymore, and here lately he seemed to be falling unconscious a lot.

"Get up" the harsh voice said. "How long have I been out this time?" Killian replied still forcing his eyes closed. He knew the moment he opened them the bright LED glow of the room he had been thrown in would immediately give him a migraine. Along with the drugs they had been pumping into his body every 12 hours. "Three days" the voice replied.

Killian finally slowly opened his eyes squinting against the bright light. He was still in his room, or cell which ever you wanted to call it. "Sean, how long are they going to keep me in here? I've told them all I know." Killian said with the tone he used to use for interrogations. "I've no idea, but we all know it's not you. You would never betray us like that. Boss wants all the bases covered though. It's unfortunate you got dragged in." Sean answered. "Marley will be in shortly" he said as he backed out of the room.

Looking around Killian noticed a box sitting on a roll away desk. Who knew what they had in store for him today.

There was deep cover, then there was in so deep you start to forget who you really are. The longer you are in the easier the lines start to blur. The mission, getting in with The Dark Ones, he had a lot riding on. And sometimes it's not easy knowing how far to go to build trust. Had he gone over that line? Definitely. Is he in some fucked up shit? For sure. The things he had done and the choices he had to make were torture enough. Add on top of that an internal investigation that would inevitably end with him being found out. He was done, mentally checked out, but at the moment his cover was still in tact. Who would ever think Robert Golds right hand man would betray them all. Everyone who had access to the location of the last FBI raid was being interrogated. Killian knew field interrogation, even enjoyed it when he was younger, he knew the tactics they were using, he even knew how to fight them. But dammit if it wasn't taking every ounce of sanity left in his mind.

They started with isolation, locking him in this dark room for days at a time. He lost count of the hours, days, weeks, sitting in the dark. After that he was taken out and personally questioned by Gold himself. Hours of questions. Hours of trying to keep his story straight. After that, they cut the lights on. The bright LED light piercing his eyes for days at a time. He was questioned again, and succeeded in keeping it all straight. Then the drugs started. It almost broke him. The Mescaline and LSD they pumped in his body almost daily was absolute torture. Forcing his mind to make him re-live so many parts of his past he wanted to bury and never think of again. Also forcing him to imagine the life he left behind and how his loved ones were coping with his loss. Did they think him dead? Was anyone looking for him? How long had it been? Emma. He couldn't think of her now. He didn't want to associate her with any of his memories of this place.

The door banged open and Killian jumped and scrambled to the corner of the room. The drugs still left in his system causing him to groan in pain at the noise. "Hook, let's go. Over here now, you know how this works" Marley huffed out. Slowly Killian got to his feet. He could feel sweat running down his face and his hands shook with tremors. His left hand, even though it shook on his best days, was barely controllable. He made his way slowly to the cot. Marley gave him the usual injections, and Killian didn't even feel the prick of the needle anymore. "Boss says you are almost in the clear, thinks he knows who the snitch is. Maybe by the end of the week you can be out of here." Marley said. Killian liked the guy for the most part. He was a younger guy probably in his mid twenties. They always had a good working relationship, and he knew it hurt him to see Killian like this. Marley walked over to the box in the corner and hit a switch, then walked out shutting and locking the door behind him.

Killian was starting to feel the first effects of the drugs slowing his body down. Then it started. The beeping, low and slow at first then slowly increasing in volume and repetition. His head was pounding the beeping slowly making his head feel as if it were going to explode. He wanted to pass out, but the mixture of the drugs, light, and noise was too much. He couldn't close his eyes, the sweat pouring off him in buckets. His body starting to fold in on itself. He was weak and tired. He tried to cover his ears, tried to block the sound out. He tried screaming to stop the defining sounds. Nothing worked. So he sat there with his hands over his ears. Repeating the same thing over and over in his head, the only thing that can keep him sane. _My name is Killian Jones. I am a special agent with the FBI. I am married to Emma Jones. I am loved. I am missed._ It seemed no matter how many times he repeated it how loud his mind yelled it at him, he started to forget and fade into the drug induced delirium his own mind created for him.

What seemed like hours later the beeping stopped. The lights went out. After a bit the ringing in his ears started to fade. Slowly the door opened a crack and then a little bit more until the whole room was lit by the light from the outside. Not the harsh lights of his room, but natural light from cloudless day. He could see trees out of the window beyond the door. Then she stepped in. He had to be hallucinating. He prayed to whatever god was out there he was hallucinating. She couldn't be here. She had to be safe. It was Emma, golden hair illuminated from behind. She looked like an angel coming to save him from this hell.

"Emma" he muttered. She slowly got closer crouching down in front of him until their noses practically touched. "Killian" she whispered "You have to keep fighting this. We are looking for you. You've got to let us know where you are, that you're alive. I need to know you're alive" His hand slowly raised to cup her cheek in his shaking grasp. She leaned into his touch and looked into his eyes. "I will find you" she said. "I always find you." with a smile and brush of her lips to his she vanished. Killian dropped his chin to his chest. Tears started to form behind his eyes, but he would not let them fall. With a shaky breath and all the strength he possessed he stood and walked towards the open door.

Minutes later he was led into the drawing room of the house Gold had them kept in. He was seated on the sofa by the unused fireplace. A glass of water was placed on the table in front of him along with a sandwich and crackers. He dove for the water and downed it in one whole gulp. "Easy lad there's plenty where that came from" he turned to his right to see Gold limping into the room cane in hand. He sat down in the seat opposite Killian.

"I'm sorry about what we've been putting you through these past few months" Gold said with a frown. "Hook, you are like a son to me. Do you know that? " Killian looked up a questioning look on his face. "It pained me to have to put you through what all the others had to go through. I can't show favoritism. You had the information that led to us losing many good men and a whole lot of business just like the rest of them. Thankfully that issue has been solved. I hope you understand that this was nothing personal." Killian looked up again in shock. He hadn't been found out? Did someone else take the fall for his treachery? Or did someone cave and admit to something they did not do? It was now or never. His next words could make him or break him. He took a breath and thought carefully about what he was going to say "I understand, it had to be done. You've helped me to become the man I am. I'm sorry I didn't realize sooner someone was giving information to the feds" his voice was rough and definitely not his own. "Good I'm glad we have an accord." Gold replied. "You may return to your normal position this coming Monday. Until then take some time, rest, see Victor to detox all those drugs from your system. Once again, I am sorry." With that Gold got to his feet and left the room.

Killian slowly got up. He was free to go? After months of this endless torture he could walk out just like that? With one foot in front of the other Killian slowly made his way out into the courtyard. A car was waiting for him to take him to his place. Killian looked around noticing every detail of the house. Fences that were over twelve foot high, and security cameras every few feet, not to mention the armed guards that were patrolling every thirty feet or so. This wasn't a house, this was a fortress. He slowly made his way to the car and slid in the back seat with a muttered "Thanks mate" to the driver. There was only one thing on his mind that really propelled him forward at that very moment. Real or hallucination Emma needed to know he was alive. He had to get her a message anything that could tip her off to his location that was so far away from Mexico City and her. He needed her to know he was ok. Now more than ever.

 _Friday July 29,2016 Georgetown, Virginia 03:54_

Emma woke with a start. Body wrapped up in blankets and sweating as if she had a fever that just broke. She saw him, dreamed of him for the first time in almost a year. She had almost forgotten what that voice with that accent sounded like. He was in pain. She could tell. His eyes sunken in and bruised from lack of sleep, or worse things they could have done to him. In her dream he was sitting on the floor of a white room, she begged him to let her know he was ok. He seemed half awake as if he were not completely there with her. She told him she would find him. That no matter what she hadn't given up on him. For the first time in a long time she felt hope.

She reached to her nightstand picking up her phone dialing as fast as she could. The voice on the other end of the line was less than pleased with the wake up call. "Ems it's four in the morning. Was it not possible to call like three hours from now?" Emma cut her friend off immediately. "Red I need you to do me a favor, it's…..It's about Killian." She heard the ruffling of sheets as Ruby sat up in bed. " What's going on Emma?" Ruby said with seriousness. " I had a dream of him. It was so real I don't know if I can even describe it. I do know I told him I'd find him. I need you to go back onto the archives and find everything you can about the raid on the compound in Mexico City. Pull fingerprints, DNA, ballistics, everything you can to help me prove he wasn't there. I'm finding him Ruby. I spent so long running from him before, I need to find him. I need to prove he had nothing to do with that day other than give us the time and place." He was alive she could feel it, he was innocent, she could feel that too. Because when you love someone you just know.


	3. Chapter 2

**A/N: Hey everyone! I am beyond sorry for the wait on this update. Holy cow real life is insane. Working a crazy schedule. This fic has not been abandoned! I have most of it mapped out its just having the time to get it out of my head. Anyways...this chapter was written while listening to Breaking Benjamin...check them out. Once again im eala-captian on tumblr! Enjoy!**

 **Disclaimer: If I wrote the show, I would have the time to update this more often!**

 _Saturday_ _July, 30 2016 Oran, Algeria 03:00_

Killian stumbled through his small apartment in the south corner of Oran. He knew he had some pain medicine around somewhere. His head was pounding. He woke up in cold sweats and with a what felt like an ice pick in the head. He really needed to make a trip to Victor or have him make a house call when the sun came up. Finally locating the Advil on the kitchen counter, he popped two into his mouth and swallowed.

"Get it together mate." He said to himself shaking his head. He had been undercover for 3 years, 2 months, 13 days. 2 years, 4 months, 8 days of which he assumed he had been labeled as missing in action, and possibly a traitor. He had so many questions. Mainly how Emma was, but he couldn't think about her without feeling completely hopeless. He had tried to make contact with her several times. It had been risky and dumb, and all failures.

Slowly, he moves around the small apartment checking nooks and corners for any bugs or cameras. Yeah he is a top ranking member of one of the biggest illegal operations in the world, but he is also an undercover mole fighting his way back to the people he loves. So blame him for being extra careful. After a thorough check of the entire apartment he deems its safe and heads back to his bedroom.

His closest is mostly the same, black t-shirts, black pants, and one or two suits for when dressing up is in order. He pushes it all aside and rummages around on the racks behind when he finally finds what he is looking for. A small easily concealed black screwdriver. Satisfied that everything is in order he closes his closet and makes his way to the patio on the opposite side of the room. He shuffles his feet and grabs hold of the bed to keep himself upright, the withdrawal of the drugs taking hold of his body and hindering his motions. Once at the door he opens it not to go outside but to slowly remove the bolts on the middle hinge. When he was forced to flee from Mexico City only a few of his possessions remained on him. His gun, the clothes he was wearing, and a small picture of his wife that he kept folded, taped between the two layers of his belt. As soon as he was dumped into Algeria he immediately found a place to store his only bit of hope. They call them slicks, small places where items can be slid in and out with ease. He had cut into the door frame and made a small hole to hold the picture.

He slowly pulls the wrinkled photo out, still folded and holds it to his chest while he reattaches the door. Making his way back to the bed he sinks into its embrace again still holding the picture to his chest before taking a deep breath. She is breathtaking. Her blond curls flowing over her shoulders, and the beautiful green eyes that pierce his heart, even though he has seen this photo one-thousand times. Tears fill his eyes as he gazes at his beautiful wife. "Love, I promise you….I'm alive...I'm….I'm trying to get back to you, but to do that I've had to do some pretty bad things. I hope you will forgive me…...I promise. God love, I swear….I will stop Gold...The Dark Ones...whoever I have to….Just please don't give up on me…..not yet...I love you so much Emma, but right now you are a weakness I can't let them exploit….So...for the time being I have to let you go...they can't...they can't figure out who you are, who I am. So from now until I'm back in your arms I have to be Hook. Killian Jones is dead. I miss you my love.

He slowly makes his way off the bed and back into the kitchen. Standing in front of the sink he opens a drawer to his left pulling out the item he needs with his ever shaking left hand. Tears blur his vision as he brings it to her beautiful face, the flames of the lighter burning a hole into his heart as the edges turn to ash. He cuts the water on slowly letting it wet the bottom of the sink as he drops his last bit of morale resolve into the sink, her smiling face disappearing among the flames. "I'll bring him back to you."

 _Saturday July 29,2016 Georgetown, Virginia 09:00_

The sudden knock on her door startled her out of her daze as she jumped up from the floor where she was sitting up a board and chart to answer. "Hey Ruby. What you got for me?" She asked as her analyst friend as she walked in the door carrying what looked like two tons of paperwork.

"I've pulled everything they would allow me. I've got crime scene photos, ballistics, fingerprints, and bullet casings. Dave said if we needed any help to call him. He is worried about you Emma." Of course David would be worried. She would be surprised if he wasn't. She had made sure to stay far away from Killians case during the initial investigation. She was too close, it was a miracle they had let them continue to work together after the nature of their relationship was made public. David had fought for them, said they worked great as a team. They were practically unstoppable, going through case after case him running tactical and her guiding his way. Robert Gold was a problem they could never seem to nail down though. So when Killian was deemed missing in action Emma stepped down. Yeah she was debriefed and asked a million questions hundreds of times, but it was as if he disappeared. Maybe..just maybe getting her own hands dirty would change the game a bit. She knew things about Killian that no one else could possibly know.

Several hours later they had come to one conclusion, they needed help. Emma reluctantly got on her phone and called Dave. There was so much intel, how could no one get anything from it.

She had looked at the same handprints, and read the same reports a hundred times. Dave finally arrived around midday with a box of pizza and a few beers. Still the work continued, until Emma finally opened the bag carrying the spent shell casings. Carefully with her gloves on she laid them all out one by one. Every casing recovered from Robert Golds team were all 9mm shells except one. Her heart dropped at the sight. Among the spent bullets she saw one 45 casing. He was there. She set the bullet down and leaned back against the couch.

"Emma, you okay?" Dave asked with a concerned look on his face.

"He was there Dave." She said looking at the ground. "He was at the ambush he fired on his own people." She looked up to see David staring at her with his mouth open. "What? How… How do you know?"

Emma and Killian had often done things off the parameters of what people would consider legal. Killian had always carried an unregistered extra weapon that had a significant meaning to him. She didn't want to tell Dave. It wasn't her story to tell, but it was important.

"Killian...he..ah...He always carried a Nighthawk Custom 45 ACP. He took it off the man who messed his hand up when he was in Special Ops for the UN." She said the last bit in a rush hoping to avoid that conversation all together. " According to the reports and photos that .45 was taken out of a wooden pillar not 3 inches from where an agent was standing. He shot at his own people Dave." David quickly got up and moved to her side she leaned into his embrace.

"Maybe someone else was carrying a .45." Ruby stated from her computer set up on Emma's dining room table. "Maybe it wasn't even him."

She noticed the file Dave was looking at sitting out in the open. "I was him." David said solemnly. Emma had been so immersed in her own find she hadn't even noticed Dave had not moved in several minutes before she set the bullets down. " I was looking over the blood prints on the walls of the compound and noticed something I hadn't seen before. Emma, Killian's hand print is at the crime scene, his left hand." Emma pulled the file towards herself across the table. Sure enough way in the background of another photo was a handprint. One that hadn't had its own picture taken of because who would have taken a picture of what looked like blood smears while searching for handprints. She could barely make out the half of hand and three fingers Killian had left.


End file.
